Nucleotide sequences from the highly variable second intron of a LEAFY homolog (a meristem identity gene) are used to delimit species and to determine the parents of hybrids and allopolyploid Isoëtes species. Our extensive sampling of sequences from diploid species and taxa of hybrid origins indicate that reticulate evolution and long distance dispersal (most probably via migratory water fowl) within the American species of Isoëtes are very common. Many of the possible permutations of hybrid evolution have been found: 1) Both diploid parental species identified (e.g., allotetraploid I. appalachiana resulted from a hybridization event between the diploid species, I. engelmannii and I. valida); 2) one of the diploid parents identified, the other diploid parent missing, either because it has not yet been collected or is extinct (both I. azorica and I. acadiensis resulted from a cross between I. engelmannii and a missing Isoëtes species); 3) both parental species are missing from our data set (e.g., allotetraploid I. hyemalis is the result of a hybridization event between two unidentified parental species); 4) the discovery of new allotetraploid species (e.g., an allotetraploid previously included in I. appalachiana is a cross between I. engelmannii and I. flaccida; 5) multiple hybridization events resulting in allopolyploid species with contributions from three or more genomes (the diploids, I. flaccida, I. 'mattaponica' in ed., and an unidentified species, all contributed to the genome of the hexaploid I. microvela from Florida); 6) a hybridization event between an allotetraploid and a diploid resulting in a new species (sequences similar to the allotetraploid I. tuckermanii and the diploid I. prototypus are found in the decaploid I. lacustris). Our data also indicate that some diploid species (e.g., I. engelmannii) contain regional variation that will probably need to be recognized at the subspecies level.

Key words: allopolyploidy, hybrid origins, Isoëtes, LEAFY intron